Charges at the district's 28 car parks - as well as on the street - were brought back in when shops reopened on Monday following a two-month suspension to support key workers.
Some business groups had called on Harrogate Borough Council and North Yorkshire County Council to extend the parking holiday, but bosses defended their decision saying it will promote social distancing and "a healthy turnover of vehicles to encourage more shoppers".
Of the 100 penalty charge notices handed out on Monday and Tuesday, 98 were on the street and two were at car parks.
The cost to motorists who park for longer than they pay for is £50.
And it is £70 for drivers who park where they shouldn't, such as in a loading bay when not loading or in a disabled bay without a blue badge.
Motorists can appeal the penalty charge notices which are also halved if paid within 14 days.
NHS staff, health or social care workers and NHS volunteer responders are still able to park for free, as long as they display their NHS permit or another valid form of evidence.
Harrogate Borough Council enforces parking in the Craven, Harrogate and Selby areas on behalf of the county council.
Providing free parking for two months during lockdown meant the borough council lost around £500,000 in parking revenue.
The authority is now facing a £15million funding shortfall as an overall result of the coronavirus crisis.
By Jacob Webster, Local Democracy Reporter